Need help with perl to encode/decode ASN.1

Joe Ryan jfryan at NHGRI.NIH.GOV
Thu Jun 10 08:20:09 EST 1999


Ray,

I have written a program which runs GENSCAN, FGENES, MZEF, GRAIL2, 
RepeatMasker, Sputnik and BLAST and prints the output as ASN.1.
Which can then be viewed graphically using NCBI's Sequin Program.

You are welcome to have a look at my code which is freely available
at http://genome.nhgri.nih.gov/genemachine/

I also found readseq to be very helpful in the process of learning ASN.1.
After converting a FASTA formatted sequence to ASN.1 using readseq, 
I was able to get an idea of the basic format.

You may also want to have a look at SEALS (or contact the author)
http://www.ncbi.nlm.nih.gov/Walker/SEALS/
I know that an ASN.1 perl module was in the works but am not sure 
on the status of this.

Oh and the on-line docs for "The DDBJ/EMBL/GenBank Feature Table Definition"
http://www.ncbi.nlm.nih.gov/collab/FT/index.html

You may also consider XML for sequence records.  There has been considerable
work done in this area and there are many freely available parsers already
available in several languages.  See these URLs for more info...
http://www.proteometrics.com/BIOML/
http://ala.vsms.nottingham.ac.uk/biodom/
http://bio.perl.org/Projects/XML/

Good Luck,

  Joe
--
Joseph Ryan
programmer
National Human Genome Research Institute

On Thu, Jun 10, 1999 at 02:50:14AM +0000, RjGrimaila wrote:
> Does anyone have experience with perl to encode/decode ASN.1 formatted records?
>  ASN.1 looks ideal for complex sequence records.  I'd like to extend existing
> perl code to save ASN.1 objects to an Oracle database.  I'm aware of 
> Convert::BER.pm, but haven't had a chance to RTFM.
> 
> RAy 
> 




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